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- PDB-4hds: Crystal Structure of ArsAB in Complex with Phenol. -

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Basic information

Entry
Database: PDB / ID: 4hds
TitleCrystal Structure of ArsAB in Complex with Phenol.
Components
  • ArsA
  • ArsB
Keywordstransferase/substrate / transferase / transferase-substrate complex
Function / homology
Function and homology information


nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process
Similarity search - Function
5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle ...5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHENOL / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSporomusa ovata (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNewmister, S.A. / Chan, C.H. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Insights into the Function of the Nicotinate Mononucleotide:phenol/p-cresol Phosphoribosyltransferase (ArsAB) Enzyme from Sporomusa ovata.
Authors: Newmister, S.A. / Chan, C.H. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ArsA
B: ArsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7605
Polymers72,5422
Non-polymers2183
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-15 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.547, 77.213, 151.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein ArsA


Mass: 36323.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporomusa ovata (bacteria) / Gene: arsA / Plasmid: pARSAB22 / Production host: Escherichia coli (E. coli) / Strain (production host): JE13607
References: UniProt: F6MZ55, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Protein ArsB


Mass: 36218.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporomusa ovata (bacteria) / Gene: arsB / Plasmid: pARSAB22 / Production host: Escherichia coli (E. coli) / Strain (production host): JE13607
References: UniProt: F6MZ56, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / pH: 7.1
Details: 13% MEPEG5K, 100 mM MOPS pH 7.1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: NI-FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→75.76 Å / Num. obs: 24812 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 26.8
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 8.7 / Rsym value: 0.528 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
SAINTdata reduction
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→75.76 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1260 5.1 %RANDOM
Rwork0.205 ---
obs0.207 24683 99.2 %-
all-25943 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å20 Å2
2--1.73 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→75.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 15 204 5006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.713
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.018
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 81 -
Rwork0.268 1458 -
obs--93.27 %

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